Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_029002077.1 H537_RS0138370 aldehyde dehydrogenase family protein
Query= metacyc::MONOMER-16244 (495 letters) >NCBI__GCF_000430725.1:WP_029002077.1 Length = 506 Score = 360 bits (923), Expect = e-104 Identities = 208/505 (41%), Positives = 293/505 (58%), Gaps = 17/505 (3%) Query: 3 LPLFVPIKLPNGTTYEQPTGLFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDD 62 + + P K +++ G FI ++V+ + F ++P T + ++ + EDI+ Sbjct: 1 MDMLEPGKFGFPVNFKKRYGNFIGGQWVEPAKGQYFENITPVTGKVFCEIPRSTEEDIER 60 Query: 63 AVEAATAAFHSSWSTSDPQVRMKVLYKLADLIDEHADTLAHIEALDNGKSLM-CSKGDVA 121 A++AA AA ++W + P R VL K+AD ++++ + LA E DNGK + D+ Sbjct: 61 ALDAAHAA-KAAWGRTSPTERAAVLLKMADRMEQNLELLATAETWDNGKPIRETMAADLP 119 Query: 122 LTAAYFRSCAGWTDKIKGSVIETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVL 181 L +FR AG +G++ E + Y EP+GV GQIIPWNFPLLMA WKL P L Sbjct: 120 LAIDHFRYFAGCVRSQEGTISEIDHQTYAYHFHEPLGVVGQIIPWNFPLLMAVWKLAPAL 179 Query: 182 CTGCTTVLKTAESTPLSALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAF 241 G VLK AE TP+S L L +I + PPGV+NVV+GFG AG P++S +I K+AF Sbjct: 180 AAGNCIVLKPAEQTPVSVLVLMEVIGDL-LPPGVLNVVNGFGVEAGKPLASSKRISKIAF 238 Query: 242 TGSTATGRHIMKAAAESNLKKVTLELGGKSPNIVF------DDADVKSTIQHLVTGIFYN 295 TG T TGR IM+ A++ NL VTLELGGKSPNI F DDA ++ N Sbjct: 239 TGETGTGRLIMQYASQ-NLIPVTLELGGKSPNIFFADVMAKDDAFFDKALEGFAM-FALN 296 Query: 296 TGEVCCAGSRIYVQEGIYDKIVSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYI 355 GEVC SR V E IYD + ++K G+P T +GAQ S QL KIL Y+ Sbjct: 297 QGEVCTCPSRALVHESIYDAFMERAIKRVAAIKAGNPLDASTMIGAQASDEQLKKILSYM 356 Query: 356 DIGKKEGATVITGGERFG-----NKGYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKT 410 DIG+ EGA V+ GGER G++IKPT+F + +I ++EIFGPV+++T FK Sbjct: 357 DIGRGEGAEVLIGGERNSLGGDLEGGFYIKPTVFKGHNK-MRIFQEEIFGPVLSVTTFKD 415 Query: 411 VEEVIALANDSEYGLAAGVHTTNLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSG 470 EE +A+AND+ +GL AGV + +++TA + I +G +W N Y+ + FGGY QSG Sbjct: 416 EEEALAIANDTNFGLGAGVWSRDMNTAFRMGRGIQAGRVWTNCYHAYPAHAAFGGYKQSG 475 Query: 471 IGREMGEEALDNYTQVKAVRIGLSQ 495 IGRE + LD+Y Q K + + S+ Sbjct: 476 IGRETHKMMLDHYQQTKNLLVSYSE 500 Lambda K H 0.316 0.133 0.389 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 588 Number of extensions: 25 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 495 Length of database: 506 Length adjustment: 34 Effective length of query: 461 Effective length of database: 472 Effective search space: 217592 Effective search space used: 217592 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory